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Gi Beom Keum,Eun Sol Kim,Jin Ho Cho,송민호,Kwang Kyo Oh,Jae Hyoung Cho,김신아,김혜리,곽진옥,두현옥,Sriniwas Pandey,김현범,이주훈 한국축산학회 2023 한국축산학회지 Vol.65 No.1
Antibiotics have been used in livestock production for not only treatment but also for increasing the effectiveness of animal feed, aiding animal growth, and preventing infectious diseases at the time when immunity is lowered due to stress. South Korea and the EU are among the countries that have prohibited the use of antibiotics for growth promotion in order to prevent indiscriminate use of antibiotics, as previous studies have shown that it may lead to increase in cases of antibiotic-resistant bacteria. Therefore, this study evaluated the number of antibiotic resistance genes in piglets staging from pre-weaning to weaning. Fecal samples were collected from 8 piglets just prior to weaning (21 d of age) and again one week after weaning (28 d of age). Total DNA was extracted from the 200 mg of feces collected from the 8 piglets. Whole metagenome shotgun sequencing was carried out using the Illumina Hi-Seq 2000 platform and raw sequence data were imported to Metagenomics Rapid Annotation using Subsystem Technology (MG-RAST) pipeline for microbial functional analysis. The results of this study did not show an increase in antibiotic-resistant bacteria although confirmed an increase in antibiotic-resistant genes as the consequence of changes in diet and environment during the experiment.
Understanding the Diversity and Roles of the Ruminal Microbiome
Keum Gi Beom,Pandey Sriniwas,Kim Eun Sol,Doo Hyunok,Kwak Jinok,Ryu Sumin,Choi Yejin,Kang Juyoun,Kim Sheena,Kim Hyeun Bum 한국미생물학회 2024 The journal of microbiology Vol.62 No.3
The importance of ruminal microbiota in ruminants is emphasized, not only as a special symbiotic relationship with ruminants but also as an interactive and dynamic ecosystem established by the metabolites of various rumen microorganisms. Rumen microbial community is essential for life maintenance and production as they help decompose and utilize fiber that is difficult to digest, supplying about 70% of the energy needed by the host and 60–85% of the amino acids that reach the small intestine. Bacteria are the most abundant in the rumen, but protozoa, which are relatively large, account for 40–50% of the total microorganisms. However, the composition of these ruminal microbiota is not conserved or constant throughout life and is greatly influenced by the host. It is known that the initial colonization of calves immediately after birth is mainly influenced by the mother, and later changes depending on various factors such as diet, age, gender and breed. The initial rumen microbial community contains aerobic and facultative anaerobic bacteria due to the presence of oxygen, but as age increases, a hypoxic environment is created inside the rumen, and anaerobic bacteria become dominant in the rumen microbial community. As calves grow, taxonomic diversity increases, especially as they begin to consume solid food. Understanding the factors affecting the rumen microbial community and their effects and changes can lead to the early development and stabilization of the microbial community through the control of rumen microorganisms, and is expected to ultimately help improve host productivity and efficiency.
Antibiotic resistance in livestock, environment and humans: One Health perspective
Sriniwas Pandey,두현옥,Gi Beom Keum,Eun Sol Kim,곽진옥,류수민,Yejin Choi,강주연,김신아,Narae Lee,Kwang Kyo Oh,Ju-Hoon Lee,김현범 한국축산학회 2024 한국축산학회지 Vol.66 No.2
Antibiotic resistance (AR) is a complex, multifaceted global health issue that poses a serious threat to livestock, humans, and the surrounding environment. It entails several elements and numerous potential transmission routes and vehicles that contribute to its development and spread, making it a challenging issue to address. AR is regarded as an One Health issue, as it has been found that livestock, human, and environmental components, all three domains are interconnected, opening up channels for transmission of antibiotic resistant bacteria (ARB). AR has turned out to be a critical problem mainly because of the overuse and misuse of antibiotics, with the anticipation of 10 million annual AR-associated deaths by 2050. The fact that infectious diseases induced by ARB are no longer treatable with antibiotics foreshadows an uncertain future in the context of health care. Hence, the One Health approach should be emphasized to reduce the impact of AR on livestock, humans, and the environment, ensuring the longevity of the efficacy of both current and prospective antibiotics.
Comparative analysis of the pig gut microbiome associated with the pig growth performance
Jun Hyung Lee,김산,Eun Sol Kim,Gi Beom Keum,두현옥,곽진옥,Sriniwas Pandey,Jae Hyoung Cho,류수민,송민호,조진호,김신아,김현범 한국축산학회 2023 한국축산학회지 Vol.65 No.4
There are a variety of microorganisms in the animal intestine, and it has been known that they play important roles in the host such as suppression of potentially pathogenic microorganisms, modulation of the gut immunity. In addition, the gut microbiota and the livestock growth performance have long been known to be related. Therefore, we evaluated the interrelation between the growth performance and the gut microbiome of the pigs from 3 different farms, with pigs of varied ages ready to be supplied to the market. When pigs reached average market weight of 118 kg, the average age of pigs in three different farms were < 180 days, about 190 days, and > 200 days, respectively. Fecal samples were collected from pigs of age of 70 days, 100 days, 130 days, and 160 days. The output data of the 16S rRNA gene sequencing by the Illumina Miseq platform was filtered and analyzed using Quantitative Insights into Microbial Ecology (QIIME)2, and the statistical analysis was performed using Statistical Analysis of Metagenomic Profiles (STAMP). The results of this study showed that the gut microbial communities shifted as pigs aged along with significant difference in the relative abundance of different phyla and genera in different age groups of pigs from each farm. Even though, there was no statistical differences among groups in terms of Chao1, the number of observed operational taxonomic units (OTUs), and the Shannon index, our results showed higher abundances of Bifidobacterium, Clostridium and Lactobacillus in the feces of pigs with rapid growth rate. These results will help us to elucidate important gut microbiota that can affect the growth performance of pigs.
Hyunok Doo,Jin Ho Cho,송민호,Eun Sol Kim,김신아,Gi Beom Keum,Jinok Kwak,Sriniwas Pandey,류수민,Yejin Choi,강주연,김현범,Ju-Hoon Lee 한국축산학회 2024 한국축산학회지 Vol.66 No.2
The Enterococcus faecium (E. faecium) strain AK_C_05 was isolated from cheonggukjang, the Korean traditional food, collected from a local market in South Korea. In this report, we presented the complete genome sequence of E. faecium strain AK_C_05. The genome of E. faecium strain AK_C_05 genome consisted of one circular chromosome (2,691,319 bp) with a guanine + cytosine (GC) content of 38.3% and one circular plasmid (177,732 bp) with a GC content of 35.48%. The Annotation results revealed 2,827 protein-coding sequences (CDSs), 18 rRNAs, and 68 tRNA genes. It possesses genes, which encodes enzymes such as alpha-galactosidase (EC 3.2.1.22), beta-glucosidase (EC 3.2.1.21) and alpha-L-arabinofuranosidase (EC 3.2.1.55) enabling efficient utilization of carbohydrates. Based on Clusters of Orthologous Groups analysis, E. faecium strain AK_C_05 showed specialization in carbohydrate transport and metabolism indicating the ability to generate energy using a variety of carbohydrates.
두현옥,Hyeri Kim,조진호,송민호,Eun Sol Kim,Jae Hyoung Cho,김신아,Gi Beom Keum,곽진옥,Sriniwas Pandey,김현범,이주훈 한국축산학회 2023 한국축산학회지 Vol.65 No.3
The Lactococcus taiwanensis strain K_LL004 was isolated from the gut of a grasshopper (Oxya chinensis sinuosa) collected from local farm in Korea. L. taiwanensis strain K_LL004 is the functional probiotic candidate with an ability to hydrolyse plant polysaccharides. The complete genome of the L. taiwanensis strain K_LL004 contains one circular chromosome (1,995,099 bp) with a guanine + cytosine (GC) content of 38.8%. Moreover, 1,929 Protein- coding sequence, 19 rRNA genes, and 62 tRNA genes were identified based on results of annotation. L. taiwanensis strain K_LL004 has a gene, which encodes hydrolytic enzymes such as beta-glucosidase and beta-xylosidase, that hydrolyzes plant polysaccharides.
Evaluation of the muscle fiber type and the muscle fat ratio of pork belly and pork shoulder butt
Hyunok Doo,Jinok Kwak,Sumin Ryu,Sheena Kim,Eun Sol Kim,Gi Beom Keum,Yejin Choi,Sriniwas Pandey,Na Rae Lee,Juyoun Kang,Jeongin Choi,Yujung Lee,Dongjun Kim,Kuk-Hwan Seol,Sun Moon Kang,In-Seon Bae,Soo-Hy 한국산업식품공학회 2023 학술대회 및 심포지엄 Vol.2023 No.11
Evaluating the Prevalence of Foodborne Pathogens in Livestock Using Metagenomics Approach
( Hyeri Kim ),( Jin Ho Cho ),( Minho Song ),( Jae Hyoung Cho ),( Sheena Kim ),( Eun Sol Kim ),( Gi Beom Keum ),( Hyeun Bum Kim ),( Ju-hoon Lee ) 한국미생물 · 생명공학회 2021 Journal of microbiology and biotechnology Vol.31 No.12
Food safety is the most important global health issue due to foodborne pathogens after consumption of contaminated food. Foodborne bacteria such as Escherichia coli, Salmonella enterica, Staphylococcus aureus, Campylobacter spp., Bacillus cereus, Vibrio spp., Yersinia enterocolitica and Clostridium perfringens are leading causes of the majority of foodborne illnesses and deaths. These foodborne pathogens often come from the livestock feces, thus, we analyzed fecal microbial communities of three different livestock species to investigate the prevalence of foodborne pathogens in livestock feces using metagenomics analysis. Our data showed that alpha diversities of microbial communities were different according to livestock species. The microbial diversity of cattle feces was higher than that of chicken or pig feces. Moreover, microbial communities were significantly different among these three livestock species (cattle, chicken, and pig). At the genus level, Staphylococcus and Clostridium were found in all livestock feces, with chicken feces having higher relative abundances of Staphylococcus and Clostridium than cattle and pig feces. Genera Bacillus, Campylobacter, and Vibrio were detected in cattle feces. Chicken samples contained Bacillus, Listeria, and Salmonella with low relative abundance. Other genera such as Corynebacterium, Streptococcus, Neisseria, Helicobacter, Enterobacter, Klebsiella, and Pseudomonas known to be opportunistic pathogens were also detected in cattle, chicken, and pig feces. Results of this study might be useful for controlling the spread of foodborne pathogens in farm environments known to provide natural sources of these microorganisms.
Kim Hyeri,Kim Eun Sol,Cho Jin Ho,Song Minho,Cho Jae Hyoung,Kim Sheena,Keum Gi Beom,Kwak Jinok,Doo Hyunok,Pandey Sriniwas,Park Seung-Hwan,Lee Ju Huck,Hyunjung Jung,Hur Tai Young,Kim Jae-Kyung,Oh Kwang 한국미생물·생명공학회 2023 Journal of microbiology and biotechnology Vol.33 No.1
The foodborne illness is the important public health concerns, and the livestock feces are known to be one of the major reservoirs of foodborne pathogens. Also, it was reported that 45.5% of foodborne illness outbreaks have been associated with the animal products contaminated with the livestock feces. In addition, it has been known that the persistence of a pathogens depends on many potential virulent factors including the various virulent genes. Therefore, the first step to understanding the public health risk of livestock feces is to identify and describe microbial communities and potential virulent genes that contribute to bacterial pathogenicity. We used the whole metagenome shotgun sequencing to evaluate the prevalence of foodborne pathogens and to characterize the virulence associated genes in pig and chicken feces. Our data showed that the relative abundance of potential foodborne pathogens, such as Bacillus cereus was higher in chickens than pigs at the species level while the relative abundance of foodborne pathogens including Campylobacter coli was only detected in pigs. Also, the microbial functional characteristics of livestock feces revealed that the gene families related to “Biofilm formation and quorum sensing” were highly enriched in pigs than chicken. Moreover, the variety of gene families associated with “Resistance to antibiotics and toxic compounds” were detected in both animals. These results will help us to prepare the scientific action plans to improve awareness and understanding of the public health risks of livestock feces.